run_grammar: Generalized Renown Analysis of Molecular variance for Mixed...

In 2eding/GRAMMAR: Generalized Renown Analysis of Molecular variance for Mixed model Analysis R package (GRAMMAR)

Generalized Renown Analysis of Molecular variance for Mixed model Analysis R package

Description

run_grammar function calculates p-value and f-value.

Usage

run_grammar(K, Y, X, VC, max_itr, num.parallel, outPath, outName)

Arguments

K	is obtained from the Kinship function
Y	is the phenotype matrix, individual x phenotype
X	is the SNP matrix, individual x snp
VC	is obtained from the varComp function
max_itr	is specifies the number of permutations.
num.parallel	Number of parallel processes or a predefined socket cluster
outPath	is a parameter that specifies the path of the result file
outName	is a parameter that specifies the name of the result file

Value

p-value and f-value

Examples

   X <- as.matrix(data.table::fread(SNPData))
   Y <- as.matrix(data.table::fread(GeneExpressionData))
   
   K <- Kinship(X)
   VC <- varComp(K, Y, X)
   
   result <- run_grammar(K, Y, X, VC, max_itr = 4, num.parallel = 2, outPath = "./testdir/", outName = "result.txt")
   

2eding/GRAMMAR documentation built on Jan. 18, 2024, 6 a.m.